Just so you know... that message is by no means an error message... its merely in information box telling you that the model you are replacing could be different than the one you are replacing.
Like TheTick said... you dont need to go so far as to naming entities. Just when you replace the part, select "re-attach mates" in the property manager and that will launch a tool to help you replace the mate entities with nothing more than a point and click effort.
You can also access this tool afterwards if you like by right-clicking on the mates folder and selecting replace mate entities.
Regards,
Jon
jgbena@yahoo.com